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Nitrogen (N) fertilizer applications are important for agricultural yield, yet not all the applied N is taken up by crops, leading to surplus N storage in soil or leaching to groundwater and surface water. Leaching loss of fertilizer N represents a cost for farmers and has consequences for human health and the environment, especially in the southern Willamette Valley, Oregon, USA, where groundwater nitrate contamination is prevalent. While improved nutrient management and conservation practices have been implemented to minimize leaching, nitrate levels in groundwater continue to increase in many long-term monitoring wells. To elucidate controls on leaching rates and N dynamics in agricultural soils across soil depths, and in response to seasonal and annual variation in management (e.g., fertilizer input amount and summer irrigation), we intensively monitored the transport of water and nitrate every two weeks for four years through the vadose zone at three depths (0.8, 1.5, and 3.0 m) in a sweet corn (maize) field. Though nitrate leaching was highly variable among lysimeters at the same depth and across years, a strong pattern emerged: annual nitrate leaching significantly decreased with depth across the study, averaging ~104 kg N ha(−1) yr(−1) near the surface (0.8 m) versus ~56 kg N ha(−1) yr(−1) in the deep soil (3.0 m), a 54% reduction in leaching between the soil layers. Even though crops were irrigated in summer, most leaching (~72% below 3.0 m) occurred during the wet fall and winter. Based on steady state assumptions, a net equivalent of ~29% of surface N inputs leached below 3.0 m into the deeper soil and groundwater, while ~44% was removed in crop harvest, indicating considerable N retention in the soil (~27% of inputs or approximately 58 kg N ha(−1) yr(−1)). The accumulation and long-term dynamics of deep soil N is a legacy of agricultural management that should be further studied to better manage and reduce nitrate loss to groundwater.

The Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) was established to investigate the form, function, and dynamics of the critical zone developed on sedimentary rocks in the Appalachian Mountains in central Pennsylvania. When first established, the SSHCZO encompassed only the Shale Hills catchment, a 0.08-km subcatchment within Shaver’s Creek watershed. The SSHCZO has now grown to include 120 km of the Shaver’s Creek watershed. With that growth, the science team designed a strategy to measure a parsimonious set of data to characterize the critical zone in such a large watershed. This parsimonious design includes three targeted subcatchments (including the original Shale Hills), observations along the main stem of Shaver’s Creek, and broad topographic and geophysical observations. Here we describe the goals, the implementation of measurements, and the major findings of the SSHCZO by emphasizing measurements of the main stem of Shaver’s Creek as well as the original Shale Hills subcatchment.

Many areas in the world are characterized by shallow soils underlain by weathered bedrock, but root-rock interactions and their implications for regolith weathering are poorly understood. To test the role of tree roots in weathering bedrock, we excavated four pits along a catena in a shale-dominated catchment at the Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in central Pennsylvania. We measured a variety of biological, physical, and chemical properties including: 1) root density, distribution, and respiration, 2) soil gas, and 3) elemental compositions, mineralogy, and morphology of soil, rock, and rock fracture fill at ridge top, mid-slope, toe-slope, and valley floor sites. As expected, root density declined rapidly with depth; nevertheless, fine roots were present in rock fractures even in the deepest, least weathered shale sampled (~ 180 cm below the land surface). Root densities in shale fractures were comparable between the ridge top and mid-slope pits. However, they were significantly lower in the toe-slope, despite increasing rock fracture densities, which is likely due to a shallower water table depth at the downslope site. Average root respiration (per mass of dry root tissue) in rock fractures was comparable to rates in the soil. Thus, the total flux of CO2 from root respiration tracked root densities, decreasing with depth. Potential microbial respiration, estimated as the laboratory C mineralization potential, was about an order of magnitude lower than measured root respiration in both the soil and shale fractures. Roots were only observed in large aperture (> 50 μm) shale fractures that were filled with particulate material. The fill in these fractures was mineralogically and geochemically similar to the lowest soil horizons with respect to clay composition, element mobility, extractable dissolved organic C (DOC), inorganic N-species, and potentially mineralizable C and N, while total C and total N values for the fracture fill were similar to the shale bedrock. In the bulk soil, depletion profiles (Al, Fe, K, Mg, and Si) relative to unweathered shale reflected characteristic weathering of illite and vermiculized chlorite to kaolinite and are similar between soils and fracture fill. Such similarities indicate that the fracture coatings are likely the result of pedogenic processes that occur at depth in the fractures rather than translocation of soil particles downward into the fractures. Overall, our data suggest that roots and fill in shale fractures down to ~ 180 cm are qualitatively similar to those in surface soil horizons. Thus, the deepest manifestation of the chemical depletion profiles observed in the pits consists of the rock fracture fill, and this fill is present at low concentrations with similarly low concentrations of fine roots.

In regions of mixed land use, some ecosystems are sinks for N pollution and others are sources. Yet, beyond this gross characterization, we have little understanding of how adjacent land-use types vary in mechanisms of N cycling and retention. This study assessed the rate and magnitude of soil N retention pathways in forest, urban, and agricultural ecosystems. Soil plots in each land use were labeled with inorganic 15N and cored at 15 min, 2 days, and 20 days following injection. Subsamples were biologically fractionated to differentiate labile and stable pools, while gross N transformations were assessed via the 15N isotope dilution method. Stable soil organic 15N formed rapidly (within 15 min) in all land uses when added as 15NH4 +, and became a proportionally larger sink for inorganic 15N over time. Forests had the lowest gross immobilization rates, but the greatest amount of stable N formation. Rapid retention of NH4 + in forests may be driven by abiotic processes, with root uptake becoming a more important mechanism of retention over time. Urban sites, on the other hand, had the highest gross microbial immobilization rates and highest root N uptake, suggesting that high short-term N retention may be due to rapid biological processing. Agricultural systems, with low root uptake and the lowest stable N formation, had little capacity for retention of added N. These apparently distinct land-use cases can be understood by synthesizing several emerging aspects of N retention theory that (1) distinguish kinetic and capacity N saturation, (2) recognize links between soil C saturation on minerals and N retention, and (3) account for rapid transfers of NH4 + to stable organic pools.

Recent identification of the widespread distribution of legacy sediments deposited in historic mill ponds has increased concern regarding their role in controlling land–water nutrient transfers in the mid-Atlantic region of the US. At Big Spring Run in Lancaster, Pennsylvania, legacy sediments now overlay a buried relict hydric soil (a former wetland soil). We compared C and N processing in legacy sediment to upland soils to identify soil zones that may be sources or sinks for N transported toward streams. We hypothesized that legacy sediments would have high nitrification rates (due to recent agricultural N inputs), while relict hydric soils buried beneath the legacy sediments would be N sinks revealed via negative net nitrification and/or positive denitrification (because the buried former wetland soils are C rich but low in O2). Potential net nitrification ranged from 9.2 to 77.9 g m−2 year−1 and potential C mineralization ranged from 223 to 1,737 g m−2 year−1, with the highest rates in surface soils for both legacy sediments and uplands. Potential denitrification ranged from 0.37 to 21.72 g m−2 year−1, with the buried relict hydric soils denitrifying an average of 6.2 g m−2 year−1. Contrary to our hypothesis, relict hydric layers did not have negative potential nitrification or high positive potential denitrification rates, in part because microbial activity was low relative to surface soils, as indicated by low nitrifier population activity, low substrate induced respiration, and low exoenzyme activity. Despite high soil C concentrations, buried relict hydric soils do not provide the ecological services expected from a wetland soil. Thus, legacy sediments may dampen N removal pathways in buried relict hydric soils, while also acting as substantial sources of NO3− to waterways.

While eutrophication is often attributed to contemporary nutrient pollution, there is growing evidence that past practices, like the accumulation of legacy sediment behind historic milldams, are also important. Given their prevalence, there is a critical need to understand how N flows through, and is retained in, legacy sediments to improve predictions and management of N transport from uplands to streams in the context of climatic variability and land-use change. Our goal was to determine how nitrate (NO3−) is cycled through the soil of a legacy-sediment-strewn stream before and after soil drying. We extracted 10.16 cm radius intact soil columns that extended 30 cm into each of the three significant soil horizons at Big Spring Run (BSR) in Lancaster, Pennsylvania: surface legacy sediment characterized by a newly developing mineral A horizon soil, mid-layer legacy sediment consisting of mineral B horizon soil and a dark, organic-rich, buried relict A horizon soil. Columns were first preincubated at field capacity and then isotopically labeled nitrate (15NO3−) was added and allowed to drain to estimate retention. The columns were then air-dried and subsequently rewet with N-free water and allowed to drain to quantify the drought-induced loss of 15NO3− from the different horizons. We found the highest initial 15N retention in the mid-layer legacy sediment (17 ± 4 %) and buried relict A soil (14 ± 3 %) horizons, with significantly lower retention in the surface legacy sediment (6 ± 1 %) horizon. As expected, rewetting dry soil resulted in 15N losses in all horizons, with the greatest losses in the buried relict A horizon soil, followed by the mid-layer legacy sediment and surface legacy sediment horizons. The 15N remaining in the soil following the post-drought leaching was highest in the mid-layer legacy sediment, intermediate in the surface legacy sediment, and lowest in the buried relict A horizon soil. Fluctuations in the water table at BSR which affect saturation of the buried relict A horizon soil could lead to great loses of NO3− from the soil, while vertical flow through the legacy-sediment-rich soil profile that originates in the surface has the potential to retain more NO3−. Restoration that seeks to reconnect the groundwater and surface water, which will decrease the number of drying–rewetting events imposed on the relict A horizon soils, could initially lead to increased losses of NO3− to nearby stream waters.